GWATCH – a backbone for working with genomes
An Internet platform created at St. Petersburg State University will help find genes associated with human diseases
Access to the genomic browser will be open – any scientist will be able to use its resources.
The GWATCH genomic browser is an Internet platform hosted on the St. Petersburg State University server for automatic data analysis in order to detect genes responsible for complex human diseases.
Medical institutions around the world are overflowing with patients with oncological, neurological diseases (Alzheimer's, Parkinson's, behavioral disorders), metabolic disorders (for example, some variants of diabetes), autoimmune diseases (such as Crohn's disease, etc.) and deadly infections (HIV/AIDS, hepatitis B and C, human papillomavirus). The deep causes of many of them are often unknown, and the treatment is mainly symptomatic. In 2003, the international project "Human Genome" was completed, which gave hope for the discovery of new ways to develop "smart" drugs and targeted therapy due to the discovery of genetic determinants regulating the susceptibility to chronic diseases. However, over the next ten years, only some of the 1,500 screening studies conducted to search for genes associated with diseases were able to identify the main genetic determinants that could be applied in therapeutic practice.
The search process is particularly complicated by the size of the data arrays obtained as a result of genome-wide association studies (GWAS) and genome–wide sequencing (whole genome sequencing, WGS) - studies aimed at creating personalized medicine. The GWATCH genomic browser is an advanced computing environment with a user-friendly interface that allows researchers to view genomic association data, confirm new associations, and discover important aspects of genetic exposure that were previously extremely difficult to identify.
The abbreviation GWATCH stands for Genome-Wide Association Tracks Chromosome Highway, which means "chromosome highway for genome-wide association search". The genomic browser is based on a dynamic operating principle that allows you to directly detect, view and evaluate the picture (pattern) of genomic associations based on extensive data arrays from GWAS and WGS. The GWATCH browser uses a graphical three-dimensional (3D) interface that simulates a bird's-eye view and allows you to view any human chromosome, identifying areas of the genome that are significant in terms of associations with specific diseases. The program is based on the principle of well-known search engines and cloud services (for example, Google, Oracle, Amazon). It allows the user to access large amounts of data and makes it possible to detect, study and confirm important genomic associations that may simply be missed when using other research tools. The GWATCH environment can be used for large-scale analysis of genomic associations for any disease. The article published today provides an example of using GWATCH to analyze data from more than 6,000 patients at risk of developing HIV/AIDS. The initial study was conducted with the financial support of the National Institutes of Health (USA) on the basis of the same epidemiological cohort, the study of which made it possible to identify the CCR5-∆32 gene – the most effective of all the detected AIDS resistance genes. It also turned out to be the most useful, since it is already used in therapeutic practice. At the same time, GWATCH allows you to view and analyze association data in a similar way for any complex disease with a hereditary component.
In addition, GWATCH will be used to check the reproducibility of the results of detecting disease genes in subsequent studies: the user can simply open an image of a new open section of the genome in the browser and assess the presence of associations in the already downloaded data.
The GWATCH browser also allows you to find a solution to a complex ethical problem that has long made it difficult to conduct research on the human genome. Scientists are convinced that information should be freely distributed in the scientific environment – this will allow them to quickly get acquainted with new data and refine them. However, the requirement of confidentiality of personal information (which in most cases is a condition for conducting a study) prevents the uploading of genetic and clinical data of patients to open Internet resources. The GWATCH genomic browser allows you to store information in the public domain, displaying only derived analysis data at the population level. Personal information of patients is not disclosed. Thus, the browser will allow you to openly publish more information without violating the confidentiality agreements that are concluded with the majority of research participants.
The GWATCH genomic browser simulates a dynamic virtual environment where the user gets the opportunity to move along the video highway along human chromosomes, using data from genome-wide association search and genome-wide sequencing to identify associations of genomic variants with complex diseases. The browser has a simple, intuitive interface designed for a wide audience: geneticist experts, students and journalists working in the scientific field. The environment can also be used by patients themselves to study their own genome for genetic associations with diseases.
The GWATCH genomic browser was developed by scientists from the F. G. Dobrzhansky Center for Genomic Bioinformatics of St. Petersburg State University. The creation of the browser was partially funded from the funds of the megagrant program of the Ministry of Education and Science of the Russian Federation. The leading scientists of the project are Anton Svitin, a leading researcher, and Professor Stefan O'Brien.
Today, the description of the GWATCH platform was published in the journal GigaScience (Svitin et al., GWATCH: a web platform for automated gene association discovery analysis, in the public domain). Access to the browser is open. Scientists around the world can use it to study genetic associations and travel along chromosomal highways. Have a nice trip!
Portal "Eternal youth" http://vechnayamolodost.ru10.11.2014